Release candidate 0.3.1

mmcdermott commented 3 months ago

Fixed #88, #101, #104, and #105 and improves test organization and coverage.

Summary by CodeRabbit

New Features
- Enhanced configuration of the autoflake hook to remove unused imports directly.
- Improved logic for renaming DataFrame columns with additional validation for the "patient_id" column.
- Expanded the load method in configuration classes with detailed examples and robust error handling for predicates.
- Introduced tests for the expand_shards command-line interface and help message functionality of aces-cli.
- Developed a testing framework for medical event data extraction, including new utility functions for testing.
Bug Fixes
- Enhanced error handling and logging for DataFrame processing and validation.
Documentation
- Improved documentation in the configuration loading process and added doctests for clarity.
Chores
- Streamlined test files by importing utility functions to promote code reuse and organization.

coderabbitai[bot] commented 3 months ago

Walkthrough

The recent changes enhance the functionality and robustness of the ACES project. Key updates include improved configuration handling in src/aces/config.py, streamlined DataFrame operations in src/aces/__main__.py, and the introduction of new testing frameworks to ensure command-line tools operate correctly. These modifications collectively aim to enhance code maintainability, facilitate better error handling, and increase test coverage, particularly focusing on command-line interface features and configuration file management.

Changes

Files	Change Summary
`.pre-commit-config.yaml`	Added `--remove-all-unused-imports` argument to `autoflake` hook for improved functionality.
`src/aces/__main__.py`, `src/aces/config.py`	Improved DataFrame handling and validation checks; refined metadata processing in configuration.
`tests/test_e2e.py`, `tests/utils.py`	Removed local functions, replaced with imports from `utils` for better code reuse and modularity.
`tests/test_expand_shards.py`, `tests/test_help_message.py`, `tests/test_meds.py`	Introduced new tests to validate CLI functionality and medical data extraction processes.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant CLI
    participant Config
    participant DataFrame

    User->>CLI: Execute command
    CLI->>Config: Load configuration
    Config->>Config: Validate metadata
    Config-->>CLI: Return configuration
    CLI->>DataFrame: Process data
    DataFrame->>DataFrame: Rename columns
    DataFrame-->>CLI: Return processed data
    CLI-->>User: Show results

Assessment against linked issues

Objective	Addressed	Explanation
Ignore a `metadata` key in configuration files to allow for more flexible metadata (#[101])	✅

Poem

🐇 In the warren of code, changes abound,
With streamlined paths and fixes profound.
A hop for the helper, a leap for the test,
In the garden of logic, we strive for the best!
So let’s cheer for the tweaks, with joy we embrace,
For each little change, we quicken our pace! 🎉

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codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 89.47368% with 2 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/aces/__main__.py	90.00%	1 Missing :warning:
src/aces/config.py	88.88%	1 Missing :warning:

Files with missing lines	Coverage Δ
src/aces/__main__.py	`94.73% <90.00%> (ø)`
src/aces/config.py	`95.50% <88.88%> (ø)`

justin13601 / ACES